The Bordeaux Bioinformatics Center (CBiB) is a Bioinformatics Core Facility that is designed to address the challenges of the genomic revolution through our bioinformatics and computational biology services and research initiatives in the following ways:
- Conducting collaborative research and providing bioinformatics solutions in cancer: the CBiB provides environment for conducting collaborative research and services, tools development, data analysis, database design, supports grant applications, training, licensing of specialized software, and help with computing capabilities.
- Cancer bioinformatics infrastructure development: The CBiB works in close collaboration with the Bordeaux University (and in particular, the Mésocentre Aquitain) at the regional level, the Institut Francais de Bioinformatique at the national level and the ELIXIR at the European level to deploy adequate infrastructure solutions
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ActivityHosting and maintenance of public software and databases:
• Hosting and maintenance of software and/or data request of users, the CBiB deploys programs or data protected by a secure access. These may include software that requires a license and cannot be made publicly available (e.g. CLC Workbench) or data that the providers do not wish to make public (ex: genome sequences under embargo).
• Development, exploitation and maintenance of databases and innovative services or international scale: through its research activities or collaborations, the CBiB develops new resources, services or databases, which are made publicly available on its website.
• Customized software development software development for cases that are not covered by publicly available tools.
• Supervision the CBiB hosts and manages permanent and contractual engineering staff and/or post-docs who develop specialized information systems (e.g. pipelines for the NGS data processing) or participate in the data analysis and interpretation (e.g. annotation of SNPs). In these projects, the CBiB also provides computational and storage resources.
• Hosting and training of users of bioinformatics programs and databases receives biologists who whish to master the use of bioinformatic tools.
• Continued education M
- M. El-Kebir, H. Soueidan, T. Hume, D. Beisser, M. Dittrich, T. Müller, G. Blin, J. Hering, M. Nikolski, L. Wessels and G. Klau,
xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model, Bioinformatics 2015, doi:
- N. Quenel-Tueux, M. Debled, J. Rudewicz, G. MacGrogan, M. Pulido, L. Mauriac, F. Dalenc, T. Bachelot, B. Lortal, C. Breton-Callu
- C. Tunon de Lara, M. Fournier, H. Bonnefoi, H. Soueidan, M. Nikolski, A. Gros, C. Daly, H. Wood, P. Rabbitts ans R. Iggo, Clinical
and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated
for large operable or locally advanced hormone-receptor-positive breast cancer, British Journal of Cancer 07/2015; DOI:
- COSMOS Consortium COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access,
Metabolomics Journal, 2015, doi: 10.1007/s11306-015-0810-y
A. Sarkar and H. Soueidan and M. Nikolski, Identification of conserved gene clusters in multiple genomes based on synteny and
homology, BMC Bioinformatics, vol 12 (Suppl 9), S18, 2011
- M. Cvijovic, H. Soueidan, D. Sherman, E. Klipp and M. Nikolski, Exploratory Simulation of Cell Ageing Using Hierarchical Models,
Genome Informatics vol. 21, pp. 114-125, 2008
- Mohammed El-Kebir, Brown University, Ben Raphael’s group, Providence, USA
- Gunnar Klau, CWI Life Sciences, Algorithmic computational biology group, Amsterdam, Netherlands
- Christoph Steinbeck, EBI, Cheminformatics and metabolism group, Wellcome Genome Campus, Hinxton, UK
- Gabriele Valiente, Technical University of Catalonia, Barcelona, Spain
- Lodweyk Wessels, The Netherlands Cancer Institute, Computational Cancer Biology, Amsterdam, Netherland